Abstract PR06: Analysis of enhancer transcription reveals novel gene regulatory networks in breast cancer

Abstract Enhancer transcription is a defining feature of active enhancers. We and others have shown that enhancers that produce transcripts (so called “eRNAs”) are more likely to (1) be associated with active chromatin marks, such as H3K4me1 and K3K27ac, (2) loop to target gene promoters, and (3) be associated with target gene activation. Thus, enhancer transcription is a good predictor of active enhancers. In this regard, we have shown that enhancer transcription can be used in the absence of any other genomic information to predict enhancers. We have used Global Run-On coupled deep sequencing (GRO-seq) in 14 different breast cancer cell lines representing the five distinct molecular subtypes of breast cancer, coupled with a computational pipeline that we have developed, to predict enhancers based solely on enhancer transcription. We found both common and unique sites of enhancer transcription across the cell lines. In addition, we observed that enhancer transcription correlates with nearest gene transcription. Unsupervised hierarchical clustering of enhancer transcription was sufficient to segregate the breast cancer cell lines into their specific molecular subtypes. Transcription factor motif analysis performed at the sites of enhancer transcription identified transcription factors that may be important for the transcriptional programs of each cell type. Transcription factors whose motifs were uniquely enriched in a specific cell type were observed to be bound at the enhancers using locus-specific ChIP-qPCR assay. siRNA-mediated knockdown of the cognate transcription factors reduced enhancer transcription and cell proliferation in those cell types. The GRO-seq data were integrated with ChIP-seq data for several histone modifications typically enriched at promoters, gene bodies, enhancers, and repressive regions of the genome. The results from these analyses provide additional support for our enhancer identification pipeline. Taken together, our analyses have revealed novel gene regulatory networks that underlie breast cancer subtype-specific biology. This work was supported by a postdoctoral fellowship from the American Cancer Society - Lee National Denim Day Fellowship to H.L.F., grants from the NIH/NIDDK and CPRIT to W.L.K. and a grant from CPRIT to the LONESTAR Consortium. Citation Format: Hector L. Franco, Anusha Nagari, Yuanxin Xi, Wenqian Li, Dana Richardson, Kaori Tanaka, Jing Li, The CPRIT LONESTAR Consortium, Michelle C. Barton, Xiaobing Shi, Khandan Keyomarsi, Mark T. Bedford, Wei Li, Sharon Y.R. Dent, W. Lee Kraus. Analysis of enhancer transcription reveals novel gene regulatory networks in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr PR06.